Need to account for "Improved access to small molecule definitions and Archive Inventories at the PDB"

[jamesmkrieger]

This has been emailed to various mailing lists and needs to be accounted for:

The wwPDB have improved access to small molecule definitions in the PDB.

Individual definitions in the Chemical Component Dictionary (CCD) and
the Biologically Interesting molecule Reference Dictionary (BIRD) are
now accessible in a new FTP tree in the PDB archive. In response to user
requests, these individual CCD and BIRD entry files can be found at
/pdb/refdata/chem_comp/ and /pdb/refdata/bird/, respectively, with the
last character hash as sub-directory.

For example:
 > /pdb/refdata/chem_comp/C/D8C/D8C.cif
 > /pdb/refdata/bird/prd/8/PRD_001068.cif

There is also improved access to information about PDB archive holdings
with new inventory data files that offer a quick overview of data in the
archive. These files are in the extensible JSON format, and can be found
under the new /pdb/holdings/ FTP tree.

The inventory lists provided include:
 > all_removed_entries.json.gz: list of removed PDB entries (obsolete,
models) with entry authors, entry title, release date, obsolete date ,
and superseding PDB ID, if any.
 > current_file_holdings.json.gz: List of released PDB entries and file
types present for each entry in the PDB Core Archive (e.g., coordinate
data, experimental data, validation report, ...)
 > obsolete_structures_last_modified_dates.json.gz: List of obsolete PDB
entries with last time of PDBx/mmCIF file modification
refdata_id_list.json.gz: List of released chemical reference entries,
content types (e.g., Chemical Component, BIRD), and last time of
reference file modification
 > released_structures_last_modified_dates.json.gz: List of released PDB
entries with last time of PDBx/mmCIF file modification
 > unreleased_entries.json.gz: List of on-hold PDB entries, entry
status, deposition date, and sequence pre-release information

The inventory (index) files historically provided in /pdb/derived_data/
will continue to be updated for the time being; they will eventually be
removed from the PDB archive. Users are encouraged to utilize these new
inventory files.

Kind Regards,

David Armstrong

-- 
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544